[2023-06-05 13:29:55,010] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:29:55,013] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:29:55,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference
[2023-06-05 13:29:56,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:29:56,250] [INFO] Task started: Prodigal
[2023-06-05 13:29:56,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg3487d16b-75d6-4ad0-86df-de87df4ba684/GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna.gz | prodigal -d GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/cds.fna -a GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:30:09,219] [INFO] Task succeeded: Prodigal
[2023-06-05 13:30:09,220] [INFO] Task started: HMMsearch
[2023-06-05 13:30:09,220] [INFO] Running command: hmmsearch --tblout GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/reference_markers.hmm GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:30:09,450] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:30:09,451] [INFO] Found 6/6 markers.
[2023-06-05 13:30:09,474] [INFO] Query marker FASTA was written to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/markers.fasta
[2023-06-05 13:30:09,475] [INFO] Task started: Blastn
[2023-06-05 13:30:09,475] [INFO] Running command: blastn -query GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/reference_markers.fasta -out GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:10,063] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:10,067] [INFO] Selected 26 target genomes.
[2023-06-05 13:30:10,068] [INFO] Target genome list was writen to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/target_genomes.txt
[2023-06-05 13:30:10,072] [INFO] Task started: fastANI
[2023-06-05 13:30:10,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg3487d16b-75d6-4ad0-86df-de87df4ba684/GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna.gz --refList GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/target_genomes.txt --output GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:30:22,292] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:22,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:30:22,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:30:22,302] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:30:22,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:30:22,302] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.995	174	793	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.9871	168	793	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.6938	132	793	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.3389	63	793	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	77.3099	62	793	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.9527	66	793	95	below_threshold
Prevotella histicola	strain=JCM 15637	GCA_000613925.1	470565	470565	type	True	76.7285	51	793	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	76.6515	73	793	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.6362	73	793	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.5442	54	793	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:30:22,304] [INFO] DFAST Taxonomy check result was written to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/tc_result.tsv
[2023-06-05 13:30:22,305] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:30:22,305] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:30:22,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/checkm_data
[2023-06-05 13:30:22,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:30:22,333] [INFO] Task started: CheckM
[2023-06-05 13:30:22,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/checkm_input GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/checkm_result
[2023-06-05 13:31:03,538] [INFO] Task succeeded: CheckM
[2023-06-05 13:31:03,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:31:03,561] [INFO] ===== Completeness check finished =====
[2023-06-05 13:31:03,562] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:31:03,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/markers.fasta)
[2023-06-05 13:31:03,565] [INFO] Task started: Blastn
[2023-06-05 13:31:03,565] [INFO] Running command: blastn -query GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee56eef-85b4-469f-af76-6c6ab7b35658/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:31:04,474] [INFO] Task succeeded: Blastn
[2023-06-05 13:31:04,478] [INFO] Selected 16 target genomes.
[2023-06-05 13:31:04,479] [INFO] Target genome list was writen to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:31:04,484] [INFO] Task started: fastANI
[2023-06-05 13:31:04,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg3487d16b-75d6-4ad0-86df-de87df4ba684/GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna.gz --refList GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/target_genomes_gtdb.txt --output GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:31:13,773] [INFO] Task succeeded: fastANI
[2023-06-05 13:31:13,786] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:31:13,786] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902800585.1	s__Prevotella sp902800585	98.2504	678	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.25	98.25	0.85	0.85	2	conclusive
GCA_902769805.1	s__Prevotella sp902769805	87.1641	568	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.56	97.56	0.77	0.77	2	-
GCA_017645645.1	s__Prevotella sp017645645	83.9923	363	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779745.1	s__Prevotella sp902779745	82.9135	406	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115435.1	s__Prevotella sp900115435	80.9208	441	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.38	96.23	0.89	0.86	8	-
GCA_016291495.1	s__Prevotella sp016291495	80.8308	446	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554145.1	s__Prevotella sp017554145	80.8185	441	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458005.1	s__Prevotella sp017458005	80.1899	381	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.28	0.86	0.86	2	-
GCA_905235835.1	s__Prevotella sp905235835	80.0993	367	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.69	0.87	0.87	2	-
GCA_900314755.1	s__Prevotella sp900314755	79.7317	374	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.08	97.39	0.87	0.79	19	-
GCA_902776195.1	s__Prevotella sp902776195	79.7199	350	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.27	97.27	0.76	0.76	2	-
GCA_017470055.1	s__Prevotella sp017470055	79.6565	367	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449675.1	s__Prevotella sp017449675	79.5579	206	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320905.1	s__Prevotella sp900320905	78.0881	193	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.15	0.89	0.79	3	-
GCA_017449495.1	s__Prevotella sp017449495	77.949	106	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251295.1	s__Prevotella sp002251295	77.5029	155	793	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.86	97.35	0.91	0.81	14	-
--------------------------------------------------------------------------------
[2023-06-05 13:31:13,789] [INFO] GTDB search result was written to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/result_gtdb.tsv
[2023-06-05 13:31:13,789] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:31:13,793] [INFO] DFAST_QC result json was written to GCA_902771475.1_Rumen_uncultured_genome_RUG11673_genomic.fna/dqc_result.json
[2023-06-05 13:31:13,793] [INFO] DFAST_QC completed!
[2023-06-05 13:31:13,793] [INFO] Total running time: 0h1m19s